I seem to remember watching a clip of AE on YouTube where Matt was talking about how Alex Jones called into the show a couple of times in the early days (and on one occasion tried to disguise his voice), and I was wondering whether anyone else was aware of this.

Alex Jones has reached by telephone more than one episode of Atheist Experience.

During one episode a few years ago, Alex used a a pseudonym, possibly "Peter". The call screener did not immediately recognize "Peter" as Alex, only that "Peter" rambled about quantum mechanics and consciousness. The call screener attempted to explain some basic facts about quantum mechanics to "Peter" and ended two calls after advising "Peter" that he may call again after taking a few minutes to focus his thoughts or topic. The call screener then realized that "Peter" was Alex. Alex called a third time, was a bit more focused, and was allowed on air.